Variant report

Variant	rs4505569
Chromosome Location	chr2:54668200-54668201
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:54663522..54666566-chr2:54666978..54670736,4	K562	blood:

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10181826	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10496030	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11125539	0.91[CEU][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11694121	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12470235	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13393949	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35636918	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56257354	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72804673	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72804674	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7419821	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7574630	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003205	chr2:54220049-54700843	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	esv2762639	chr2:54220049-54700855	Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv1011790	chr2:54220049-54714553	Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv1002891	chr2:54227005-54682169	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv535722	chr2:54227005-54682169	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv1011690	chr2:54255361-54700843	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4505569	VRK2	cis	cerebellum	SCAN
rs4505569	ERLEC1	cis	cerebellum	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54660200-54668200	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr2:54664800-54668800	Enhancers	Skeletal Muscle Male	skeletal muscle
3	chr2:54665000-54668400	Enhancers	Brain Substantia Nigra	brain
4	chr2:54665000-54668600	Enhancers	Adipose Nuclei	Adipose
5	chr2:54665200-54668400	Enhancers	Brain Hippocampus Middle	brain
6	chr2:54665400-54668600	Enhancers	Fetal Muscle Leg	muscle
7	chr2:54666600-54668200	Enhancers	Primary hematopoietic stem cells	blood
8	chr2:54666600-54668400	Enhancers	Primary hematopoietic stem cells short term culture	blood
9	chr2:54666800-54668200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr2:54666800-54668400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr2:54667200-54668400	Enhancers	Brain Angular Gyrus	brain
12	chr2:54667200-54668600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr2:54667200-54668600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr2:54667200-54668600	Enhancers	Brain Anterior Caudate	brain
15	chr2:54667200-54668800	Enhancers	Brain Inferior Temporal Lobe	brain
16	chr2:54667600-54668600	Enhancers	HSMMtube	muscle
17	chr2:54667600-54673400	Weak transcription	Lung	lung
18	chr2:54667800-54671400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr2:54667800-54671600	Weak transcription	HepG2	liver
20	chr2:54667800-54673400	Weak transcription	Brain Cingulate Gyrus	brain
21	chr2:54667800-54673400	Weak transcription	Left Ventricle	heart
22	chr2:54667800-54673400	Weak transcription	Right Atrium	heart
23	chr2:54668000-54670600	Weak transcription	Fetal Heart	heart
24	chr2:54668000-54673200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr2:54668200-54668400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr2:54668200-54668600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr2:54668200-54668600	Enhancers	Skeletal Muscle Female	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links